1. Gene Ontology Luis Tari

2. Gene Ontology (GO) URL: http://www.geneontology.org/http://www.geneontology.org/ Gene Ontology is A hierarchy of roles of genes and gene products independent of any organism. Composed of three independent ontologies: molecular function, biological process, cellular component GO itself does not contain any information on genes or gene products

3. GO annotations http://www.geneontology.org/GO.current.ann otations.shtml http://www.geneontology.org/GO.current.ann otations.shtml Curators annotate their findings of genes (known as annotations) by utilizing GO for various organisms (about 20 of them). Different kinds of evidence codes Annotations with IEA (inferred from electronic annotation) evidence code are not manually verified (Least reliable)

4. GO Molecular Function Ontology Describes activities, such as catalytic or binding activities, that can be performed by individual gene products or assembled complexes of gene products at the molecular level. Example of activities transporter activity Genes that enable the directed movement of substances (such as macromolecules, small molecules, ions) into, out of, within or between cells. Example of binding insulin receptor binding Genes that interact with insulin receptors

5. GO Biological Process Ontology Defined as a biological objective to which the gene or gene product contributes. Examples cell proliferation Genes that are responsible for the multiplication or reproduction of cells, resulting in the rapid expansion of a cell population. learning/memory Genes that e acquisition and processing of information and/or the storage and retrieval of this information over time.

6. GO Cellular Component Ontology Refers to the place in the cell where the gene product is active. Examples bud nucleus cell membrane

7. GO An example showing a partial hierarchy of the Gene Ontology that involves the term apoptosis. Snapshot taken from the TGen GOBrowser.

8. Example of a gene product A gene product has one or more molecular functions and is used in one or more biological processes; it might be associated with one or more cellular components. An example showing all occurrences of SODC in the Gene Ontology from the human annotation.

9. Common applications of GO Analysis of microarray data Finding genes with similar functions Utilize biological process ontology Evaluation of protein-protein interactions Proteins are likely to interact if they are in the same location Utilize cellular component ontology

10. Extension to Ontology? We know that APOE is involved in Alzheimer’s disease. Based on the Gene Ontology annotation, APOE is involved in “learning and/or memory” biological process. If we ask “is the gene APOE related to Alzheimer’s disease?” Yes, because APOE is known to be involved in “learning and/or memory”. BUT there is NO ontology that says learning and/or memory can influence Alzheimer’s disease Degradation of ubiquitin cycle can cause extra long/short half-life of genes Extra long/short half-life of genes can cause cancer